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Biodiv-compose

This proxies and consolidates other Rapid Automated Biodiversity Risk Assessments intallations.

View it live.

Runing individual apps:

How to run

Required data

It is important that you have:

  • A published checklist in IPT
  • Published occurrences in one or many IPTs

Preparing

You will need at least 4GB of RAM and it is recommended 50GB of disk and 4 cores, but it varies with the data to load.

Install Git, and latest Docker and docker-compose.

Clone the repository:

$ git clone https://github.com/biodivdev/rrapp-compose $ cd rrapp-compose

For latest elasticsearch you might need to configure the machine with the following:

$ sudo sysctl -w vm.max_map_count=262144

Configuration and Customization

By default it will bind to port 8080, it can be changed at config/Caddyfile (not the Caddyfile at root, the one at config directory), you can also add a domain and automatic HTTPS, see caddy documentation for other options.

The file config/dwc-bot.list is a list of IPT's where to get the data from.

The file config/config.ini is the configuration of all apps:

  • ELASTICSEARCH=http://elasticsearch:9200 tells which elasticsearch to use
  • INDEX=dwc Tells which index to use on the elasticsearch
  • LOOP=true Tells for the bot and the index to keep runing timely (auto-update the data)
  • SOURCE=lista_flora_do_brasil Tells the name of the resource to use as taxonomic backbone

Running

Download the images of the apps (important to keep up-to-date):

$ docker-compose pull

Start them all:

$ docker-compose up -d

They will start in background. You can follow the logs with:

$ docker-compose logs

License

MIT